QC APP

Introduction

Welcome to your [QCPName] Quality Control Analysis Report! We are pleased to present to you a visual QC summary of your dataset. Representing high-dimensional omics data using plots helps us view large amounts of information at once to identifying patterns and trends across your samples and datasets. The "[QCP Name]" package monitors metrics based on the input datasets provided. For any concerns about or suggestions to improve this report, let the team know at GroupHeartBioinformaticsSupport@cshs.org, and we will consider your feedback. We are happy to support your computational needs.

The report is divided into 2 tabs:

  • ID-Free - When a mzML directory is provided as input, ID-Free Tab is populated with plots from ID-Free parameters extracted from your mzML files.
  • ID-Based - When a protein, peptide or precursor level intensity file is provided, ID-based Tab will be populated with ID-based parameters extracted from your quantified input.

ID-Free Metrics

The following ID-Free metrics have been extracted from mzML files. Provided thresholds have been applied and outlier analysis has been performed. If no outliers were found, outlier plots will not be plotted.

Total Ion Current

The total ion current (TIC) is the summed intensity across the entire range of masses being detected in each sample. MS1 and MS2 Total Ion Current Values extracted from spectra within the given mzML files

TIC Outliers

MS1 TIC is expected to be consistent across QC samples. Any outliers detected are highlighted in yellow. Outliers detected could point to issues with sample pickup or samples being dried out. Please check the specific samples listed below.

3 outliers were found. The following files have been detected as outliers: 20211018_Seroconversion_DBS_Plate1_DR4_centroid.mzML, 20211018_Seroconversion_DBS_Plate6_DR4_centroid.mzML, 20211018_Seroconversion_DBS_Plate8_DR2_centroid.mzML

MS2 TIC is expected to be consistent across QC samples. Any outliers detected are highlighted in yellow. Outliers detected could point to issues with sample pickup or samples being dried out. Please check the specific samples listed below.

3 outliers were found. The following files have been detected as outliers: 20211018_Seroconversion_DBS_Plate1_DR4_centroid.mzML, 20211018_Seroconversion_DBS_Plate6_DR4_centroid.mzML, 20211018_Seroconversion_DBS_Plate8_DR2_centroid.mzML

Groupwise TIC CV%

When a grouping file is provided, CV% for TIC values across samples in each group is calculated. This provides an insignt into how consistent the samples are within each group.

CV% for MS1 TIC was calculated using TIC values from each sample within a provided group. All groups have passed the CV Threshold

CV% for MS2 TIC was calculated using TIC values from each sample within a provided group. All groups have passed the CV Threshold


Spectral Ratio

The number of spectra recorded in each mzML file is extracted. The spectral ratio represents the number of MS2 Spectra over the number of MS1 Spectra found in each file.

Max Base Peak Intensity

The base peak intensity is the recorded intensity of the most intense peak from each spectrum in the mzML file. The Max Base Peak Intensity represents the highest recorded base peak intensity in each mzML file.

Max Base Peak Intensity is expected to be consistent across QC samples. Any outliers detected are highlighted in yellow. Outliers detected could point to issues with sample pickup or samples being dried out. Please check the specific samples listed below.

1 outliers were found. The following files have been detected as outliers: 20211018_Seroconversion_DBS_Plate1_DR3_centroid.mzML

ID-Based Metrics

The following metrics have been calculated and derived from the input search results that were provided. Given input thresholds have been applied and if grouping file was provided, groupwise comparison has also been performed.


Protein Quantification

Number of proteins identified from each sample. Any sample not meeting the threshold could indicate an issue within sample preparation or digestion protocols.

Precursor Quantification

Number of precursors identified from each sample. Any sample not meeting the threshold could indicate an issue within sample preparation or digestion protocols.


Intensity CV% Cumulative Frequency

Cumulative Frequency % of calculated CV% across all samples

Percentage of Proteins Under CV%

Intensity CV% across samples within each group is calculated. Threshold is set to 70.0% of proteins under 40.0 CV%

Percentage of Precursors Under CV%

Intensity CV% across samples within each group is calculated. Threshold is set to 70.0% of precursors under 40.0 CV%


PCA for Protein Intensities

PCA plot from protein intensities across provided groups. If any grouping/clustering is observed, please check for batch effects across the provided groups.

PCA for Precursor Intensities

PCA plot from precursor intensities across provided groups. If any grouping/clustering is observed, please check for batch effects across the provided groups.


Common Precursor TIC

The Total Ion Current here is calculated from intensities of common precursors found in all samples. Any inconsistent patterns could indicate problems in sample preparation.

Common Precursor TIC Group CV%

Common Precursor TIC CV% calculated from intensities of common precursors within each provided group. A CV% higher than the set threshold of 40.0 indicates an inconsistency within the samples of the group.


Percent Miscleavage

Total Number of 0 miscleaved peptides found in each sample. If the percentage of 0 miscleaved peptides is under the miscleavage threshold value of 80.0%, this could indicate issues with sample preparation and digestion protocols.